`nerd nmr_deg_kinetics`

nerd nmr_deg_kinetics fits first-order degradation rates (k_deg) for NMR reactions registered via nmr_create. Each reaction needs a decay_trace file recorded in the database trace list.

nerd nmr_deg_kinetics --config PATH/TO/config.yaml --db PATH/TO/nerd.sqlite

If --db is omitted, the CLI uses <run.output_dir>/nerd.sqlite.

Configuration Layout

run:
  label: nmr_deg_demo
  output_dir: examples
  backend: local

nmr_deg_kinetics:
  search_roots:
    - ../../test_data
  plugin: lmfit_deg
  plugin_options:
    model: exponential
  fit_params:
    normalize: true
  reaction_ids: [1, 2, 3]

Key Fields

Field	Description
`search_roots`	Directories to resolve trace paths when they are relative.
`plugin`	Registered degradation fit engine (`lmfit_deg` is the default).
`plugin_options`	Passed to the engine constructor (e.g., choose a different model).
`fit_params`	Forwarded to the plugin’s `fit` call; allows run-specific overrides.
`reaction_ids`	Optional explicit reactions to fit. Leave empty to fit every degradation reaction in the database.

Prerequisites

Ingest reactions via nerd nmr_create, including trace mappings: yaml trace_files: decay_trace: nmr_degradation_data/dms_schwalbe_25C_rep1.csv
Ensure constructs, buffers, and sequencing runs exist in the database (nerd create).

Outputs

Rows in nmr_fit_runs with plugin, model, and reaction metadata.
Associated nmr_fit_params capturing k_value, k_error, r2, chisq, etc.
JSON summaries under <output_dir>/<label>/nmr_deg_kinetics_latest/results/.

Examples

# Fit all degradation reactions
nerd nmr_deg_kinetics --config examples/nmr_fit_deg/configs/fit_deg.yaml                        --db examples/nerd.sqlite

# Fit a subset of reaction IDs
nerd nmr_deg_kinetics --config configs/fit_deg_subset.yaml --db nerd.sqlite

Once the fits are recorded, Arrhenius analysis can reuse them via tempgrad_fit with data_source: nmr.